Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.
These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital.
Access through NCBI Virus
You can access GenBank virus sequences, annotations, and metadata for all viruses in our archive, including Alphainfluenza virus, via NCBI Virus. A variety of filters are available to select sequences that match your research interests, and many fields of metadata are normalized to make data comparisons easier. For example, the following set of filter terms will provide all H5N1 sequences from the U.S. from December 1, 2023, to May 16, 2024, which were isolated from human hosts (Figure 1). To search for sequences from specific sample types such as milk, use the isolation source filter.
Figure 1: NCBI Virus Influenza Data Hub browser filtered for H5N1 sequences collected between December 1, 2023, and May 16, 2024, in the USA that were isolated from human hosts. Selected filters shown on the left-hand side of the image. The browser shows a much larger set of H5N1 sequences isolated from cattle.
Coming soon! We are working on providing influenza genomes consisting of a full set of segments grouped by sample metadata, and they will soon be available through NCBI Virus. Stay tuned for more information.
Need command-line access? Check out NCBI Datasets!
Access data programmatically with the NCBI Datasets datasets and dataformat command-line tools. Use genus name (Alphainfluenzavirus), taxid (197911) or NCBI Nucleotide accession. You can filter by date, host, and geographic location. See our help documentation on command-line access to get started. You can also refer to the Alphainfluenza virus documentation for further details:
Do you have Influenza virus sequence data? Submit to NCBI!
You can submit your influenza virus sequence data reads to the Sequence Read Archive (SRA) or assembled genome data to GenBank using the NCBI Submission Portal. Influenza viruses have a dedicated submission process (no annotation file necessary), and submissions are typically processed within hours.
If you plan to submit large volumes of sequences to GenBank and would prefer to submit using a command line option, please contact the GenBank Team by email at gb-admin@ncbi.nlm.nih.gov for instructions on creating and submitting through an FTP account.
If you have questions or concerns about submitting data to SRA, please contact our SRA Team by email at sra@ncbi.nlm.nih.gov.
Learn more
For more information on HN51 bird flu, visit the CDC website.
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